add pdb matching function

[LilySnow]

pdb matching is a very useful step for pdb analysis. It would be nice if we could add this to pdb2sql.

Expected performance:

INPUT:

• a reference pdb file with multiple chains
• a set of pdb files for the same protein complex but with different numbering and chain IDs

OUTPUT:

• chain ID mapping
• pdb files renumbered based on the reference pdb. Chain IDs are also changed based on the reference pdb

Ideally, we hope to separate pdb_matching into two functions (steps):

Step 1. pdb_match_chn_batch.py: match chain IDs of pdb files to ref.pdb. Output _newChnID.pdb files. Note: This step can be skipped if model.pdb files have already matched chain IDs. This step is also error-prone when multiple chains are highly similar to each other. Therefore, a human visual check is necessary.

Step 2. pdb_renum_batch.py: align and renumber pdb files to ref.pdb. Output _renum.pdb files.

There are two existing solutions:

1. https://github.com/LilySnow/PDB-matching (python + cpp)
2. https://github.com/DeepRank/haddock-tools/commit/ed9beee4437a58ecf9dbc7961b38a63cb5b9e282 (python, by the haddock group)

Maybe we could use these solutions as the basis?

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